"There's trouble, they're playing a game I think," a man who did not want to be named said.

"The last probably five years Margie wanted to get a job in the school but... the school won't allow it."

Mr Samson, when questioned about the allegation, admitted he believed the school should employ more local people.

"The system is you must have a police clearance for anyone, whether it's Margie or someone else... I wonder if the white staff actually have a police clearance as well," he said.

"The main big thing in this community is unemployment and that's the reality.

"When you start coming out and looking at remote communities, closing the gap is not there for us... for someone [local] to be able to become a principal of the school down the track, or become a doctor... education is a key to that and it's not happening."

But Mr Samson's fight to have more local people employed at the school has meant the educational outcomes of the community's children has begun to suffer.

In 2015, the school was boasting its attendance rate had jumped as high as 80 per cent after long struggle with high truancy rates.

It credited a new teaching method called direct instruction for the change – a new program championed by Cape York leader Noel Pearson, and supported by Mr Samson.

Mr Samson told The Australian in March 2015 that before the new program was introduced, he had not stood foot in a classroom in his community in 20 years because he was so disappointed by the low standards reached there.

"A few years ago, in the last mining boom, we had talks with big mining companies and they were going to employ our young people but they came back and said, 'Sorry, their literacy and numeracy is not up to standard'," he said.

"It was so dis­appointing and a big wake-up for a lot of us. I thought, 'This can't go on', and that's when we started looking for a new way."

Since his comments, yearly attendance averages at Jigalong Remote Community School have dropped from 62.8 per cent in 2015 to 33 per cent in 2016.

Department deputy director general of schools, David Axworthy said he would like to see families sending their children back to the school.

"I understand there is unrest in the community and it's unfortunate that the operations of the school are being affected, along with a number of other community services," he said.

"The Department is working with the Department of Aboriginal Affairs and Federal Government to organise a community meeting and find a resolution.

"At the end of the day, children need to go to school. It's not only the law, it's also vital to children's personal development and future prospects."

The anonymous community member, who has family members at the school, said the rest of the community had "had enough" and that the students wanted to go back to school.

But Mr Samson has given no indication when he will let that occur.

"You must remember these kids, they actually have a culture of authority by the elders... therefore if some elders decided to say this is what we're going to do, they respect it... because it's a cultural value," he said.

Jigalong's Martu people have one of Australia's most ancient cultures and hold dear the traditions of desert life. There are some Martu elders still alive who can recall the first time they saw a white man.

However, the living conditions in many Martu communities are Third World. Some Martu children go hungry, rarely attend school and are at risk of abuse from alcohol-affected people.

Since the Jigalong school's principal, Mr Wilson, was employed in February 2015, five staff members have come to the end of their remote teaching service contracts, while two have completed six months and decided to relocate to other remote communities.

The transient nature of teachers in such a remote area is not unusual, but Mr Samson claimed it showed others were also unhappy with Mr Wilson.

WA Labor MP and chairperson of the Martu Schools Alliance, Alannah MacTiernan, described the situation at the school as "tragic" and urged Mr Samson to allow the children to return to school.

"My strong counsel to Brian would be get the children back into school... but as a matter of principle in these remote communities, there must be regard had to very strongly held opinions about the appointment of a principal," she said.

"The tragedy of all this is that Brian was the person that really pushed direct instruction because he was so unhappy with the lack of education that was being delivered to the kids across the Western Desert... he got the whole ball rolling."

The Federal Government's ninth Closing the Gap report, released on Tuesday, showed Indigenous school attendance rates continued to decrease with remoteness.

In 2016, the attendance rate for Indigenous students fell from 86.9 per cent in inner regional areas to 66.4 per cent in very remote areas.

State and federal governments are on track to meet just one of seven targets in the Closing the Gap strategy, with setbacks in the areas of employment and child mortality and desired improvement only in the number of Indigenous students finishing year 12.

The Department of Education declined to comment on allegations against Mr Wilson made by Mr Samson.